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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ), 'gf_id' => 'HOM05D001227', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001227' ), 'data_identifier' => 'HOM05D001227', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001227', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p01650' => 'bna', 'A03p05760' => 'bna', 'A03p37460' => 'bna', 'A04p14840' => 'bna', 'A04p18890' => 'bna', 'A05p04590' => 'bna', 'A10p25170' => 'bna', 'A10p29600' => 'bna', 'Aa31LG1G25990' => 'aar', 'Aa31LG3G14640' => 'aar', 'Aa31LG3G6320' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3235' => 'aag', 'Actinidia06315' => 'ach', 'Actinidia07962' => 'ach', 'Actinidia15858' => 'ach', 'Actinidia21573' => 'ach', 'Actinidia21574' => 'ach', 'Actinidia22025' => 'ach', 'Actinidia31700' => 'ach', 'Actinidia32334' => 'ach', 'Actinidia32335' => 'ach', 'Actinidia39372' => 'ach', 'Actinidia40437' => 'ach', 'Ah.04g152410' => 'amhyb', 'Ah.04g152620' => 'amhyb', 'Ah.04g161700' => 'amhyb', 'Ah.06g193320' => 'amhyb', 'Ah.13g075970' => 'amhyb', 'Ah.13g075980' => 'amhyb', 'AL3G23790' => 'aly', 'AL6G16890' => 'aly', 'AL6G23610' => 'aly', 'Aqoxy1G00173' => 'aox', 'Aqoxy1G00511' => 'aox', 'Aqoxy2G00084' => 'aox', 'arahy.Tifrunner.gnm1.ann1.72M7T5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7EE83P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JN769R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3DPW3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NTGG2H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TU0730' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUWD5T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UV84TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V7V4BZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VMQ9W0' => 'arhy', 'AT2G44440' => 'ath', 'AT3G12140' => 'ath', 'AT5G06780' => 'ath', 'AT5G13020' => 'ath', 'ATR0605G153' => 'atr', 'ATR0605G319' => 'atr', 'ATR0697G183' => 'atr', 'Atru.chr11.2691' => 'acertr', 'Atru.chr2.1518' => 'acertr', 'Atru.chr3.2432' => 'acertr', 'Atru.chr3.2435' => 'acertr', 'Atru.chr8.1084' => 'acertr', 'AUR62000052' => 'cqu', 'AUR62012044' => 'cqu', 'AUR62019224' => 'cqu', 'AUR62024312' => 'cqu', 'BcaB01g03309' => 'bca', 'BcaB01g05382' => 'bca', 'BcaB02g08815' => 'bca', 'BcaB02g08819' => 'bca', 'BcaB03g16382' => 'bca', 'BcaB04g18695' => 'bca', 'BcaB04g21094' => 'bca', 'BcaB06g25537' => 'bca', 'BcaC01g01685' => 'bca', 'BcaC01g04063' => 'bca', 'BcaC01g04094' => 'bca', 'BcaC01g05170' => 'bca', 'BcaC02g12314' => 'bca', 'BcaC05g29285' => 'bca', 'BcaC06g32393' => 'bca', 'BcaC06g32543' => 'bca', 'BcaC09g48216' => 'bca', 'BcaNung01179' => 'bca', 'BcaNung01856' => 'bca', 'BolC1t05262H' => 'bol', 'BolC3t13177H' => 'bol', 'BolC3t15306H' => 'bol', 'BolC4t22172H' => 'bol', 'BolC5t34233H' => 'bol', 'BolC9t59245H' => 'bol', 'BolC9t59740H' => 'bol', 'BraA02t05144Z' => 'bra', 'BraA03t09915Z' => 'bra', 'BraA03t11687Z' => 'bra', 'BraA04t17122Z' => 'bra', 'BraA05t19433Z' => 'bra', 'BraA10t44579Z' => 'bra', 'BraA10t45002Z' => 'bra', 'C01p53170' => 'bna', 'C01p53180' => 'bna', 'C02p05860' => 'bna', 'C03p06710' => 'bna', 'C03p29580' => 'bna', 'C04p05320' => 'bna', 'C05p55640' => 'bna', 'C09p64080' => 'bna', 'C09p69980' => 'bna', 'CAN.G1023.2' => 'can', 'CAN.G167.6' => 'can', 'CAN.G261.20' => 'can', 'CAN.G364.6' => 'can', 'CANSAT11G2417' => 'cansat', 'CANSAT54G0326' => 'cansat', 'CANSAT64G2717' => 'cansat', 'CARHR086710' => 'chi', 'CARHR139600' => 'chi', 'CARHR200440' => 'chi', 'CARHR206400' => 'chi', 'Carub.0003s1149' => 'cru', 'Carub.0004s2702' => 'cru', 'Carub.0006s0567' => 'cru', 'Carub.0006s1119' => 'cru', 'Ca_02926_v3' => 'car', 'Ca_08313_v3' => 'car', 'Ca_08514_v3' => 'car', 'Ca_11300_v3' => 'car', 'Ca_11954_v3' => 'car', 'Ca_25703_v3' => 'car', 'CBR_g20979' => 'cbr', 'Cc02_g27110' => 'ccan', 'Cc06_g16060' => 'ccan', 'CDE04G2356' => 'cde', 'CDE06G2572' => 'cde', 'CDE07G0504' => 'cde', 'CDE07G1860' => 'cde', 'CDE07G1878' => 'cde', 'CDE10G1275' => 'cde', 'Cfa009659' => 'cfa', 'Cfa010716' => 'cfa', 'Cfa020180' => 'cfa', 'Ciclev10011900m.g' => 'ccl', 'Ciclev10015259m.g' => 'ccl', 'Ciclev10020940m.g' => 'ccl', 'Ciclev10031573m.g' => 'ccl', 'CiPaw.09G031200' => 'cil', 'CiPaw.13G001100' => 'cil', 'CiPaw.13G168400' => 'cil', 'CiPaw.14G126600' => 'cil', 'ClCG03G013660' => 'cla', 'ClCG09G003820' => 'cla', 'ClCG10G017440' => 'cla', 'COL.COLO4_10391' => 'col', 'COL.COLO4_23912' => 'col', 'COL.COLO4_28643' => 'col', 'COL.COLO4_36153' => 'col', 'COL.COLO4_36159' => 'col', 'COL.COLO4_37541' => 'col', 'Cpa.g.sc117.2' => 'cpa', 'Cpa.g.sc189.25' => 'cpa', 'Cpa.g.sc85.77' => 'cpa', 'CsaV3_1G042390' => 'csa', 'CsaV3_3G038920' => 'csa', 'CsaV3_7G031410' => 'csa', 'CSS0007047' => 'camsi', 'CSS0011037' => 'camsi', 'CSS0016005' => 'camsi', 'CSS0026773' => 'camsi', 'CSS0038253' => 'camsi', 'CSS0042270' => 'camsi', 'CSS0042320' => 'camsi', 'CSS0044005' => 'camsi', 'DCAR_002028' => 'dca', 'DCAR_013555' => 'dca', 'DCAR_017014' => 'dca', 'DCAR_029618' => 'dca', 'Dinv13789' => 'din', 'Dinv14283' => 'din', 'Dinv14284' => 'din', 'Dinv15835' => 'din', 'Dinv24085' => 'din', 'Dinv29041' => 'din', 'Dinv43487' => 'din', 'Dinv43927' => 'din', 'Duzib093G0432' => 'dzi', 'Duzib128G1681' => 'dzi', 'Duzib150G0579' => 'dzi', 'Duzib168G1128' => 'dzi', 'Duzib170G0861' => 'dzi', 'Duzib268G1184' => 'dzi', 'ECA233G1561' => 'eca', 'ECA234G3791' => 'eca', 'ECA236G4298' => 'eca', 'ECA248G2433' => 'eca', 'EL10Ac3g06929' => 'bvu', 'EL10Ac4g10323' => 'bvu', 'Eucgr.B02599' => 'egr', 'Eucgr.B03648' => 'egr', 'Eucgr.G03407' => 'egr', 'Eucgr.K01833' => 'egr', 'FAN01G1127' => 'fan', 'FAN01G2873' => 'fan', 'FAN02G3592' => 'fan', 'FAN03G1938' => 'fan', 'FAN05G4166' => 'fan', 'FAN06G0848' => 'fan', 'FAN07G0158' => 'fan', 'FAN09G0684' => 'fan', 'FAN09G3620' => 'fan', 'FAN11G2860' => 'fan', 'FAN12G3810' => 'fan', 'FAN14G0549' => 'fan', 'FAN14G1253' => 'fan', 'FAN16G0846' => 'fan', 'FAN17G0550' => 'fan', 'FAN21G0936' => 'fan', 'FAN22G1018' => 'fan', 'FAN25G1953' => 'fan', 'FvH4_3g44080' => 'fve', 'FvH4_4g24150' => 'fve', 'FvH4_6g03210' => 'fve', 'FvH4_6g22490' => 'fve', 'FvH4_7g00190' => 'fve', 'Glyma.02G178800' => 'gma', 'Glyma.08G149700' => 'gma', 'Glyma.09G000500' => 'gma', 'Glyma.09G112500' => 'gma', 'Glyma.10G296332' => 'gma', 'Glyma.12G240400' => 'gma', 'Glyma.15G269700' => 'gma', 'Glyma.19G117000' => 'gma', 'Glyma.20G246900' => 'gma', 'Gohir.A04G048600' => 'ghi', 'Gohir.A05G066764' => 'ghi', 'Gohir.A08G012800' => 'ghi', 'Gohir.A13G214900' => 'ghi', 'Gohir.D04G098200' => 'ghi', 'Gohir.D05G069600' => 'ghi', 'Gohir.D08G023200' => 'ghi', 'Gohir.D13G218600' => 'ghi', 'Gorai.004G018500' => 'gra', 'Gorai.006G067000' => 'gra', 'Gorai.009G070600' => 'gra', 'Gorai.013G249400' => 'gra', 'GSVIVG01001373001' => 'vvi', 'GSVIVG01025353001' => 'vvi', 'GSVIVG01029959001' => 'vvi', 'GSVIVG01033513001' => 'vvi', 'HanXRQChr05g0132851' => 'han', 'HanXRQChr13g0404231' => 'han', 'HanXRQChr16g0520441' => 'han', 'HanXRQChr17g0560601' => 'han', 'HanXRQChr17g0560611' => 'han', 'Haze_03263' => 'cav', 'Haze_19974' => 'cav', 'Haze_23029' => 'cav', 'Hma1.2p1_0183F.1_g080810' => 'hma', 'Hma1.2p1_0417F.1_g148890' => 'hma', 'HPP92_000462' => 'vpl', 'HPP92_002975' => 'vpl', 'HPP92_002982' => 'vpl', 'HPP92_002988' => 'vpl', 'HPP92_005862' => 'vpl', 'HPP92_005864' => 'vpl', 'HPP92_015757' => 'vpl', 'HPP92_015759' => 'vpl', 'HPP92_017812' => 'vpl', 'Hund03680' => 'sun', 'Hund07553' => 'sun', 'Hund19197' => 'sun', 'Hund21660' => 'sun', 'Lalb_Chr01g0008131' => 'lal', 'Lalb_Chr02g0144401' => 'lal', 'Lalb_Chr03g0033891' => 'lal', 'Lalb_Chr18g0047821' => 'lal', 'Lalb_Chr18g0047831' => 'lal', 'Lalb_Chr19g0131981' => 'lal', 'Lalb_Chr21g0307641' => 'lal', 'Lalb_Chr21g0316061' => 'lal', 'Lalb_Chr22g0358711' => 'lal', 'Lalb_Chr22g0358721' => 'lal', 'Lalb_Chr22g0358731' => 'lal', 'Lj1A438G30' => 'lonja', 'Lj1g0024583' => 'lja', 'Lj3g0001890' => 'lja', 'Lj3g0015046' => 'lja', 'Lj3g0023165' => 'lja', 'Lj5g0022082' => 'lja', 'Lj5g0024870' => 'lja', 'Lj6g0009139' => 'lja', 'Lj7A564T38' => 'lonja', 'Lj9A623G51' => 'lonja', 'Lju124A28G36' => 'lonja', 'Lju124A28G37' => 'lonja', 'Lsat_1_v5_gn_2_101160' => 'lsa', 'Lsat_1_v5_gn_2_23261' => 'lsa', 'Lsat_1_v5_gn_2_27560' => 'lsa', 'Lsat_1_v5_gn_3_124300' => 'lsa', 'Lsat_1_v5_gn_4_46360' => 'lsa', 'Lsat_1_v5_gn_5_18100' => 'lsa', 'Lsat_1_v5_gn_5_19500' => 'lsa', 'Lsat_1_v5_gn_6_49820' => 'lsa', 'Lsat_1_v5_gn_8_74320' => 'lsa', 'Manes.06G169500' => 'mes', 'Manes.08G045800' => 'mes', 'Manes.08G046100' => 'mes', 'Manes.09G034400' => 'mes', 'Manes.09G136700' => 'mes', 'Manes.14G015400' => 'mes', 'Manes.16G063500' => 'mes', 'Mapoly0008s0163' => 'mpo', 'Mapoly0069s0030' => 'mpo', 'MBI01_g33893_MAGBIO' => 'mbi', 'MBI04_g46410_MAGBIO' => 'mbi', 'MBI11_g05434_MAGBIO' => 'mbi', 'MCO09G400' => 'mco', 'MD02G1318200' => 'mdo', 'MD03G1018600' => 'mdo', 'MD07G1003100' => 'mdo', 'MD11G1019600' => 'mdo', 'MD11G1020100' => 'mdo', 'MD12G1058900' => 'mdo', 'MD14G1008100' => 'mdo', 'MD14G1059100' => 'mdo', 'Medtr1g053905' => 'mtr', 'Medtr2g060720' => 'mtr', 'Medtr4g022860' => 'mtr', 'Medtr4g100880' => 'mtr', 'Medtr7g086660' => 'mtr', 'Medtr7g093070' => 'mtr', 'MELO3C009636.2' => 'cme', 'MELO3C015674.2' => 'cme', 'MELO3C023516.2' => 'cme', 'Migut.B01366' => 'egut', 'Migut.K00042' => 'egut', 'Migut.N01646' => 'egut', 'MSTRG.10838' => 'ama', 'MSTRG.17062' => 'ama', 'MSTRG.26089' => 'ama', 'Nitab4.5_0000266g0010' => 'nta', 'Nitab4.5_0000324g0250' => 'nta', 'Nitab4.5_0000346g0050' => 'nta', 'Nitab4.5_0000892g0060' => 'nta', 'Nitab4.5_0003792g0040' => 'nta', 'Nitab4.5_0003890g0040' => 'nta', 'Nitab4.5_0004606g0010' => 'nta', 'Nitab4.5_0008087g0010' => 'nta', 'Nn2g14558' => 'nnu', 'Nn2g15649' => 'nnu', 'Nn7g36024' => 'nnu', 'Oeu007770.1' => 'oeu', 'Oeu013588.1' => 'oeu', 'Oeu014568.1' => 'oeu', 'Oeu046520.1' => 'oeu', 'Oeu053536.1' => 'oeu', 'Oeu063561.1' => 'oeu', 'Os04g0659400' => 'osa', 'Os08g0328300' => 'osa', 'Os08g0510500' => 'osa', 'Os09g0279000' => 'osa', 'Os10g0436850' => 'osa', 'Peaxi162Scf00081g00218' => 'pax', 'Peaxi162Scf00258g00315' => 'pax', 'Peaxi162Scf00878g00328' => 'pax', 'PGR102G1817' => 'pgr', 'PGR119G0991' => 'pgr', 'PGR142G1337' => 'pgr', 'PGSC0003DMG400020770' => 'stu', 'PGSC0003DMG401018219' => 'stu', 'PGSC0003DMG402006332' => 'stu', 'PGSC0003DMG402018219' => 'stu', 'Phvul.001G105300' => 'pvu', 'Phvul.005G039400' => 'pvu', 'Phvul.007G003300' => 'pvu', 'Phvul.007G259000' => 'pvu', 'Phvul.011G214500' => 'pvu', 'Potri.001G013800' => 'ptr', 'Potri.001G229000' => 'ptr', 'Potri.003G212300' => 'ptr', 'Potri.006G191400' => 'ptr', 'Potri.009G022900' => 'ptr', 'Potri.016G047600' => 'ptr', 'Potri.T070080' => 'ptr', 'Pp3c16_11440' => 'ppa', 'Prupe.2G004600' => 'ppe', 'Prupe.6G017900' => 'ppe', 'Prupe.7G014800' => 'ppe', 'Prupe.7G075700' => 'ppe', 'Psat0s3568g0080' => 'psa', 'Psat0s4178g0040' => 'psa', 'Psat0s5414g0040' => 'psa', 'Psat3g068800' => 'psa', 'Psat7g232560' => 'psa', 'PSO170G5352' => 'pso', 'PSO339G0172' => 'pso', 'PSO384G2814' => 'pso', 'PSO541G1289' => 'pso', 'PSO675G2046' => 'pso', 'QL01p009115' => 'qlo', 'QL04p000099' => 'qlo', 'QL04p003119' => 'qlo', 'QL04p003123' => 'qlo', 'QL07p023440' => 'qlo', 'RcHm_v2.0_Chr1g0313441' => 'rch', 'RcHm_v2.0_Chr3g0479901' => 'rch', 'RcHm_v2.0_Chr4g0430921' => 'rch', 'RcHm_v2.0_Chr5g0080381' => 'rch', 'Rhsim01G0132700' => 'rsi', 'Rhsim01G0187000' => 'rsi', 'Rhsim03G0007400' => 'rsi', 'Rhsim07G0050700' => 'rsi', 'Sabra01G0010000' => 'sbr', 'Sabra03G0155300' => 'sbr', 'Sabra06G0146600' => 'sbr', 'Sabra09G0014400' => 'sbr', 'Sabra16G0051000' => 'sbr', 'Sabra16G0136600' => 'sbr', 'SalBow1G0584' => 'sbo', 'SalBow1G1478' => 'sbo', 'SalBow5G3760' => 'sbo', 'Sc13g0002240' => 'sci', 'Sc16g0011920' => 'sci', 'Sed0000740' => 'sed', 'Sed0002233' => 'sed', 'Sed0006975' => 'sed', 'Sed0010632' => 'sed', 'Sed0010692' => 'sed', 'Sed0015711' => 'sed', 'SEGI_07798' => 'sgi', 'SEGI_15902' => 'sgi', 'SEGI_21594' => 'sgi', 'SGA_v2.0_scaffold274G46475' => 'sas', 'SGA_v2.0_scaffold4G02236' => 'sas', 'SGA_v2.0_scaffold94G28427' => 'sas', 'SGA_v2.0_scaffold95G28778' => 'sas', 'SHI16024' => 'shi', 'SHI16026' => 'shi', 'SHI30527' => 'shi', 'SMO117G0211' => 'smo', 'SMO164G0157' => 'smo', 'SMO339G0017' => 'smo', 'Solyc01g073960.4' => 'sly', 'Solyc03g063280.3' => 'sly', 'Solyc06g009900.3' => 'sly', 'Solyc10g044960.3' => 'sly', 'Sopen01g033530' => 'spe', 'Sopen03g015840' => 'spe', 'Sopen06g004570' => 'spe', 'Sopen10g014770' => 'spe', 'Sp3g10370' => 'spa', 'Sp4g26510' => 'spa', 'Sp6g30950' => 'spa', 'Sp6g36070' => 'spa', 'TAR369G0562' => 'tar', 'TAR623G0835' => 'tar', 'TAR623G1718' => 'tar', 'TAR633G0495' => 'tar', 'TAR633G1049' => 'tar', 'TAR636G0302' => 'tar', 'TAR636G2589' => 'tar', 'THA.LOC104799086' => 'tha', 'THA.LOC104799300' => 'tha', 'THA.LOC104809928' => 'tha', 'THA.LOC104811122' => 'tha', 'THA.LOC104827579' => 'tha', 'Thecc.01G416100' => 'tca', 'Thecc.05G170100' => 'tca', 'Thecc.05G241800' => 'tca', 'Thecc.09G219200' => 'tca', 'Thhalv10001461m.g' => 'esa', 'Thhalv10013727m.g' => 'esa', 'Thhalv10014235m.g' => 'esa', 'Thhalv10020983m.g' => 'esa', 'TPR.G14351' => 'tpr', 'TPR.G24591' => 'tpr', 'TPR.G27749' => 'tpr', 'TPR.G33017' => 'tpr', 'TPR.G34783' => 'tpr', 'TPR.G40597' => 'tpr', 'TPR.G5631' => 'tpr', 'TWI09G0581' => 'twi', 'TWI32G0680' => 'twi', 'TWI32G1240' => 'twi', 'TWI60G0071' => 'twi', 'TWI73G0540' => 'twi', 'TWI74G1601' => 'twi', 'TWI77G0177' => 'twi', 'unitig_0.g1371' => 'ugi', 'unitig_0.g1964' => 'ugi', 'unitig_26.g8837' => 'ugi', 'unitig_26.g9594' => 'ugi', 'unitig_61.g26440' => 'ugi', 'unitig_749.g13485' => 'ugi', 'unitig_750.g28430' => 'ugi', 'vmacro07927' => 'vma', 'vmacro12700' => 'vma', 'vmacro13620' => 'vma', 'vmacro21160' => 'vma', 'vmacro23233' => 'vma', 'VMungo0720G0622' => 'vmu', 'VMungo0720G0740' => 'vmu', 'VMungo1080G0656' => 'vmu', 'VMungo1127G1626' => 'vmu', 'VMungo1383G2705' => 'vmu', 'Zm00001eb047570' => 'zma', 'Zm00001eb094380' => 'zma', 'Zm00001eb101940' => 'zma', 'Zm00001eb177390' => 'zma', 'Zm00001eb199900' => 'zma', 'Zm00001eb308560' => 'zma', 'Zm00001eb316790' => 'zma' ) $gf_id = 'HOM05D001227' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001227' ) $data_identifier = 'HOM05D001227' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 6, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 19, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 9, 'sun' => (int) 4, 'lal' => (int) 11, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 9, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb316790' $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